def build_bb(self):
"""Build backbone for residue."""
if self.prev_res is None:
self.bb = self._init_bb()
else:
pts = [self.prev_res.bb[0], self.prev_res.bb[1], self.prev_res.bb[2]]
for j in range(4):
if j == 0:
# Placing N
t = self.prev_res.ang[4] # thetas["ca-c-n"]
b = BB_BUILD_INFO["BONDLENS"]["c-n"]
pb = BB_BUILD_INFO["BONDLENS"]["ca-c"] # pb is previous bond len
dihedral = self.prev_res.ang[1] # psi of previous residue
elif j == 1:
# Placing Ca
t = self.prev_res.ang[5] # thetas["c-n-ca"]
b = BB_BUILD_INFO["BONDLENS"]["n-ca"]
pb = BB_BUILD_INFO["BONDLENS"]["c-n"]
dihedral = self.prev_res.ang[2] # omega of previous residue
elif j == 2:
# Placing C
t = self.ang[3] # thetas["n-ca-c"]
b = BB_BUILD_INFO["BONDLENS"]["ca-c"]
pb = BB_BUILD_INFO["BONDLENS"]["n-ca"]
dihedral = self.ang[0] # phi of current residue
else:
# Placing O (carbonyl)
t = torch.tensor(BB_BUILD_INFO["BONDANGS"]["ca-c-o"])
b = BB_BUILD_INFO["BONDLENS"]["c-o"]
pb = BB_BUILD_INFO["BONDLENS"]["ca-c"]
if self.is_last_res:
# we explicitly measure this angle during dataset creation,
# no need to invert it here.
dihedral = self.ang[1]
else:
# the angle for placing oxygen is opposite to psi of current res
dihedral = self.ang[1] - np.pi
next_pt = nerf(pts[-3],
pts[-2],
pts[-1],
b,
t,
dihedral,
l_bc=pb,
nerf_method=self.nerf_method)
pts.append(next_pt)
self.bb = pts[3:]
return self.bb
def _init_bb(self):
"""Initialize the first 3 points of the protein's backbone.
Placed in an arbitrary plane (z = .001).
"""
n = torch.tensor([0, 0, 0.001], device=self.device)
ca = n + torch.tensor([BB_BUILD_INFO["BONDLENS"]["n-ca"], 0, 0],
device=self.device)
cx = torch.cos(np.pi - self.ang[3]) * BB_BUILD_INFO["BONDLENS"]["ca-c"]
cy = torch.sin(np.pi - self.ang[3]) * BB_BUILD_INFO["BONDLENS"]['ca-c']
c = ca + torch.tensor(
[cx, cy, 0], device=self.device, dtype=torch.float32)
o = nerf(n, ca, c, torch.tensor(BB_BUILD_INFO["BONDLENS"]["c-o"]),
torch.tensor(BB_BUILD_INFO["BONDANGS"]["ca-c-o"]),
self.ang[1] - np.pi) # opposite to current residue's psi
return [n, ca, c, o]
def build_sc(self):
"""Build the sidechain atoms for this residue.
Care is taken when placing the first sc atom (the beta-Carbon). This is
because the dihedral angle that places this atom must be defined using a
neighboring (previous or next) residue.
"""
assert len(self.bb) > 0, "Backbone must be built first."
self.atom_names = ["N", "CA", "C", "O"]
self.pts = {"N": self.bb[0], "CA": self.bb[1], "C": self.bb[2]}
if self.next_res:
self.pts["N+"] = self.next_res.bb[0]
else:
self.pts["C-"] = self.prev_res.bb[2]
last_torsion = None
for i, (pbond_len, bond_len, angle, torsion, atom_names) in enumerate(
_get_residue_build_iter(self.name, SC_BUILD_INFO)):
# Select appropriate 3 points to build from
if self.next_res and i == 0:
a, b, c = self.pts["N+"], self.pts["C"], self.pts["CA"]
elif i == 0:
a, b, c = self.pts["C-"], self.pts["N"], self.pts["CA"]
else:
a, b, c = (self.pts[an] for an in atom_names[:-1])
# Select appropriate torsion angle, or infer if part of a planar configuration
if type(torsion) is str and torsion == "p":
torsion = self.ang[SC_ANGLES_START_POS + i]
elif type(torsion) is str and torsion == "i" and last_torsion is not None:
torsion = last_torsion - np.pi
new_pt = nerf(a,
b,
c,
bond_len,
angle,
torsion,
l_bc=pbond_len,
nerf_method=self.nerf_method)
self.pts[atom_names[-1]] = new_pt
self.sc.append(new_pt)
last_torsion = torsion
self.atom_names.append(atom_names[-1])
return self.sc